Equus Genomes And The Study Of Fast Chromosomal Evolution

Horses and donkey are recognized as extremely successful domestic animals. Humans in many parts of the world have relied on them for thousands of years. They have many excellent physiological characteristics, and the relationship between them has attracted wide interest for species separation and hybridization applications. Furthermore, karyotypic diversification is more prominent in Equus species than in other mammals. So, Equus is a promising model for exploring karyotypic instability. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski’s horse), a male domestic horse (Mongolian horse), a donkey and an Asiatic wild ass. Portion of Y chromosome from wild horse assemblies (3M bp) and Mongolian horse (2M bp) were also sequenced and de novo assembled.Donkeys show a steady demographic trajectory, which was extremely dynamic for the horse. Our results reflect the distinct characteristics, including effective energy metabolism and better immunity ability, of donkeys, which are in contrast to the animated disposition and greater athletic ability of horses. Our results also reveal severe genetic bottlenecks in wild horse genome.The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is for less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. We detected abundant satellite sequences in some inactive old centromere regions but not in neocentromere regions. In contrast, ribosomal RNAs frequently emerged in neocentromere regions but not in the inactive old centromere regions. Expanded miRNA families and five newly discovered miRNAs in donkey target genes, which are involved in meiosis, have been identified. These miRNAs may associate with fast karyotype evolution. APC/C. which controls sister chromatid segregation. cytokinesis and the establishment of the G1 phase of the cell cycle, was identified by analysis of miRNA targets and rapidly evolving genes.The analysis results of these representative Equus species improved the genomic maps of the Equus. Our comparative analysis based on these genomic sequences provides important insight into the demographic history and adaptive evolution of Equus. It also revealed the unique aspects of the chromosomal rearrangement and improved our understanding of chromosomal evolution in mammals implicating Equus is thus a promising model to explore the karyotypic instability. These analysis and discoveries would benefit studies of mammal karyotypic evolution and chromosomal rearrangement, and studies of human disease caused by chromosome aberration.